Genome-wide association studies on growth performance trait of Nigerian indigenous Chicken genotypes
Abstract
Meat from Nigerian indigenous chickens (NICs) has high consumer demands but slow growth rate with high variability in body weight (BW). A study was carried out at T&R farm of FUNAAB identifying chromosomes associated with body weights of NICs in a GWAS study using the chicken 60K Single Nucleotide Polymorphisms (SNPs) Panel for 53313 markers subjected to test. Body weight was taken for 8 week. Blood samples were collected from 42 purebreds and F2 upgrades of NICs to extract DNA and amplify through PCR-RFLP technique to obtain Amplicons used for sequencing. Sequenced molecular analysis involving many Molecular software packages and bioinformatics approach were were done to trim and compare the sequence. The raw phenotypic data which comprised of the sex and body weight (>2 kg as 1 (case)) and <1 kg as 0 (control)) were analyzed using Gen Abel of the R Software Package to carry out quality checks through some filtering techniques on these chickens. The results from Selective sweep analysis identified ten chromosomes and SNPs associated with BWT of the NICs F2 upgrades Nigerian Chickens resource population. However, ten chromosomes with SNPs associated with BWT at the suggestive Bonferroni significant threshold level (p < 0.05) were discovered. These findings made it clear that F2 upgrades had better trait association on chromosomes when compared to those of the Purebreds and should be included as a genetic marker in the breeding programs by breeders for genetic improvement due to the potentialities found in this NICs genotypes studied.